. Author manuscript; available in PMC: 2010 Aug 1.

Published in final edited form as: J Comput Chem. 2009 Aug;30(11):1701–1711. doi: 10.1002/jcc.21268

Table 3.

Relative binding energies to benzamidine (Ligand A) from explicit and implicit solvent calculations (kcal/mol). See Table 1 for references for the experimental values. The experimental data from the same source were used for ligands B, C and D. For ligand E, we used the more recent data.⁵⁹

	A→B	A→C	A→D	A→E
Experimental	1.6	1.5	−0.6/−0.9	1.6
Explicit FEP (this work)	1.8	1.8	−0.3	1.3
MM-PMPB (this work)	1.9	5.5	−1.2	1.6
QM/MM-PB/SA¹	−0.6	−0.1	NA	NA
QM/MM-PB/SA²	0.6	0.6	NA	NA
PB/SA³	1.9	NA	0.70	NA

Table 1 in Ref 39. Flexible trypsin.

Table 2 in Ref39. Rigid trypsin.

Table 1 in Ref67.